[
  {
    "panel_section_name": "Collection Operations",
    "xrefs": [],
    "description": "",
    "is_workflow_compatible": true,
    "labels": [],
    "help": "<p>This tool takes a paired dataset collection and builds two datasets from it. If mapped over a list of paired datasets, this tool will produce two lists of datasets.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>If a collection consists of two forward and two reverse datasets (e.g., forward and reverse reads from a sequencing experiment) this tool will output two collections: one consisting of forward reads and one of reverse reads.<\/p>\n<p class=\"infomark\">This tool will create new history datasets from your collection but your quota usage will not increase.<\/p>\n",
    "edam_operations": [],
    "form_style": "regular",
    "edam_topics": [],
    "panel_section_id": "collection_operations",
    "version": "1.0.0",
    "link": "/tool_runner?tool_id=__UNZIP_COLLECTION__",
    "target": "galaxy_main",
    "min_width": -1,
    "model_class": "UnzipCollectionTool",
    "hidden": "",
    "id": "__UNZIP_COLLECTION__",
    "name": "Unzip Collection"
  },
  {
    "panel_section_name": "Collection Operations",
    "xrefs": [],
    "description": "",
    "is_workflow_compatible": true,
    "labels": [],
    "help": "<p>This tool takes two datasets and creates a dataset pair from them. Mapping over two lists, this tool can be used to build a list of dataset pairs from two individual lists of datasets.<\/p>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>If you have one collection containing only forward reads and one containing only reverse, this tools will &quot;zip&quot; them together into a simple paired collection.<\/p>\n<p class=\"infomark\">This tool will create new history datasets for your collection but your quota usage will not increase.<\/p>\n",
    "edam_operations": [],
    "form_style": "regular",
    "edam_topics": [],
    "panel_section_id": "collection_operations",
    "version": "1.0.0",
    "link": "/tool_runner?tool_id=__ZIP_COLLECTION__",
    "target": "galaxy_main",
    "min_width": -1,
    "model_class": "ZipCollectionTool",
    "hidden": "",
    "id": "__ZIP_COLLECTION__",
    "name": "Zip Collection"
  },
  {
    "panel_section_name": "Collection Operations",
    "xrefs": [],
    "description": "datasets from a collection",
    "is_workflow_compatible": true,
    "labels": [],
    "help": "<p>This tool takes a dataset collection and filters out datasets in the failed state. This is useful for continuing a multi-sample analysis when one of more of the samples fails at some point.<\/p>\n<p class=\"infomark\">This tool will create new history datasets from your collection but your quota usage will not increase.<\/p>\n",
    "edam_operations": [],
    "form_style": "regular",
    "edam_topics": [],
    "panel_section_id": "collection_operations",
    "version": "1.0.0",
    "link": "/tool_runner?tool_id=__FILTER_FAILED_DATASETS__",
    "target": "galaxy_main",
    "min_width": -1,
    "model_class": "FilterFailedDatasetsTool",
    "hidden": "",
    "id": "__FILTER_FAILED_DATASETS__",
    "name": "Filter failed"
  },
  {
    "panel_section_name": "Collection Operations",
    "xrefs": [],
    "description": "datasets from a collection",
    "is_workflow_compatible": true,
    "labels": [],
    "help": "<p>This tool takes a dataset collection and filters out empty datasets. This is useful for continuing a multi-sample analysis when downstream tools require datasets to have content.<\/p>\n<p class=\"infomark\">This tool will create new history datasets from your collection but your quota usage will not increase.<\/p>\n",
    "edam_operations": [],
    "form_style": "regular",
    "edam_topics": [],
    "panel_section_id": "collection_operations",
    "version": "1.0.0",
    "link": "/tool_runner?tool_id=__FILTER_EMPTY_DATASETS__",
    "target": "galaxy_main",
    "min_width": -1,
    "model_class": "FilterEmptyDatasetsTool",
    "hidden": "",
    "id": "__FILTER_EMPTY_DATASETS__",
    "name": "Filter empty"
  },
  {
    "panel_section_name": "Lift-Over",
    "xrefs": [],
    "description": "between assemblies and genomes",
    "is_workflow_compatible": true,
    "labels": [],
    "help": "<p class=\"warningmark\">Make sure that the genome build of the input dataset is specified (click the pencil icon in the history item to set it if necessary).<\/p>\n<p class=\"warningmark\">This tool can work with interval, GFF, and GTF datasets. It requires the interval datasets to have chromosome in column 1,\nstart co-ordinate in column 2 and end co-ordinate in column 3. BED comments\nand track and browser lines will be ignored, but if other non-interval lines\nare present the tool will return empty output datasets.<\/p>\n<hr class=\"docutils\" />\n<p class=\"infomark\"><strong>What it does<\/strong><\/p>\n<p>This tool is based on the LiftOver utility and Chain track from <a class=\"reference external\" href=\"http://genome.ucsc.edu/\">the UC Santa Cruz Genome Browser<\/a>.<\/p>\n<p>It converts coordinates and annotations between assemblies and genomes. It produces 2 files, one containing all the mapped coordinates and the other containing the unmapped coordinates, if any.<\/p>\n<blockquote>\n<\/blockquote>\n<hr class=\"docutils\" />\n<p><strong>Example<\/strong><\/p>\n<p>Converting the following hg16 intervals to hg18 intervals:<\/p>\n<pre class=\"literal-block\">\nchrX  85170   112199  AK002185  0  +\nchrX  110458  112199  AK097346  0  +\nchrX  112203  121212  AK074528  0  -\n<\/pre>\n<p>will produce the following hg18 intervals:<\/p>\n<pre class=\"literal-block\">\nchrX  132991  160020  AK002185  0  +\nchrX  158279  160020  AK097346  0  +\nchrX  160024  169033  AK074528  0  -\n<\/pre>\n",
    "edam_operations": [],
    "form_style": "regular",
    "edam_topics": [],
    "panel_section_id": "liftOver",
    "version": "1.0.6",
    "link": "/tool_runner?tool_id=liftOver1",
    "target": "galaxy_main",
    "min_width": -1,
    "model_class": "Tool",
    "hidden": "",
    "id": "liftOver1",
    "name": "Convert genome coordinates"
  }
]